Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures

Antarctic fish belonging to Notothenioidei represent an extraordinary example of radiation in the cold. In addition to the absence of hemoglobin, icefish show a number of other striking peculiarities including large-diameter blood vessels, high vascular densities, mitochondriarich muscle cells, and unusual mitochondrial architecture. In order to investigate the bases of icefish adaptation to the extreme Southern Ocean conditions we sequenced the complete genome of the icefish Chionodraco myersi. Comparative analyses of the icefish genome with those of other teleost species, including two additional white-blooded and five red-blooded notothenioids, provided a new perspective on the evolutionary loss of globin genes. Muscle transcriptome comparative analyses against red-blooded notothenioids as well as temperate fish revealed the peculiar regulation of genes involved in mitochondrial function in icefish. Gene duplication and promoter sequence divergence were identified as genome-wide patterns that likely contributed to the broad transcriptional program underlying the unique features of icefish mitochondria

Long-lasting effects of chronic exposure to chemical pollution on the hologenome of the Manila clam

Chronic exposure to pollutants affects natural populations, creating specific molecular and biochemical signatures. In the present study, we tested the hypothesis that chronic exposure to pollutants might have substantial effects on the Manila clam hologenome long after removal from contaminated sites. To reach this goal, a highly integrative approach was implemented, combining transcriptome, genetic and microbiota analyses with the evaluation of biochemical and histological profiles of the edible Manila clam Ruditapes philippinarum, as it was transplanted for 6 months from the polluted area of Porto Marghera (PM) to the clean area of Chioggia (Venice lagoon, Italy). One month post‐transplantation, PM clams showed several modifications to its resident microbiota, including an overrepresentation of the opportunistic pathogen Arcobacter spp. This may be related to the upregulation of several immune genes in the PM clams, potentially representing a host response to the increased abundance of deleterious bacteria. Six months after transplantation, PM clams demonstrated a lower ability to respond to environmental/physiological stressors related to the summer season, and the hepatopancreas‐associated microbiota still showed different compositions among PM and CH clams. This study confirms that different stressors have predictable effects in clams at different biological levels and demonstrates that chronic exposure to pollutants leads to long‐lasting effects on the animal hologenome. In addition, no genetic differentiation between samples from the two areas was detected, confirming that PM and CH clams belong to a single population. Overall, the obtained responses were largely reversible and potentially related to phenotypic plasticity rather than genetic adaptation. The results here presented will be functional for the assessment of the environmental risk imposed by chemicals on an economically important bivalve species

The highly rearranged mitochondrial genomes of the crabs Maja crispata and Maja squinado (Majidae) and gene order evolution in Brachyura

Abstract We sequenced the mitochondrial genomes of the spider crabs Maja crispata and Maja squinado (Majidae, Brachyura). Both genomes contain the whole set of 37 genes characteristic of Bilaterian genomes, encoded on both \u3b1- and \u3b2-strands. Both species exhibit the same gene order, which is unique among known animal genomes. In particular, all the genes located on the \u3b2-strand form a single block. This gene order was analysed together with the other nine gene orders known for the Brachyura. Our study confirms that the most widespread gene order (BraGO) represents the plesiomorphic condition for Brachyura and was established at the onset of this clade. All other gene orders are the result of transformational pathways originating from BraGO. The different gene orders exhibit variable levels of genes rearrangements, which involve only tRNAs or all types of genes. Local homoplastic arrangements were identified, while complete gene orders remain unique and represent signatures that can have a diagnostic value. Brachyura appear to be a hot-spot of gene order diversity within the phylum Arthropoda. Our analysis, allowed to track, for the first time, the fully evolutionary pathways producing the Brachyuran gene orders. This goal was achieved by coupling sophisticated bioinformatic tools with phylogenetic analysis

U and Th content in the Central Apennines continental crust: a contribution to the determination of the geo-neutrinos flux at LNGS

The regional contribution to the geo-neutrino signal at Gran Sasso National Laboratory (LNGS) was determined based on a detailed geological, geochemical and geophysical study of the region. U and Th abundances of more than 50 samples representative of the main lithotypes belonging to the Mesozoic and Cenozoic sedimentary cover were analyzed. Sedimentary rocks were grouped into four main "Reservoirs" based on similar paleogeographic conditions and mineralogy. Basement rocks do not outcrop in the area. Thus U and Th in the Upper and Lower Crust of Valsugana and Ivrea-Verbano areas were analyzed. Based on geological and geophysical properties, relative abundances of the various reservoirs were calculated and used to obtain the weighted U and Th abundances for each of the three geological layers (Sedimentary Cover, Upper and Lower Crust). Using the available seismic profile as well as the stratigraphic records from a number of exploration wells, a 3D modelling was developed over an area of 2^{\circ}x2^{\circ} down to the Moho depth, for a total volume of about 1.2x10^6 km^3. This model allowed us to determine the volume of the various geological layers and eventually integrate the Th and U contents of the whole crust beneath LNGS. On this base the local contribution to the geo-neutrino flux (S) was calculated and added to the contribution given by the rest of the world, yielding a Refined Reference Model prediction for the geo-neutrino signal in the Borexino detector at LNGS: S(U) = (28.7 \pm 3.9) TNU and S(Th) = (7.5 \pm 1.0) TNU. An excess over the total flux of about 4 TNU was previously obtained by Mantovani et al. (2004) who calculated, based on general worldwide assumptions, a signal of 40.5 TNU. The considerable thickness of the sedimentary rocks, almost predominantly represented by U- and Th- poor carbonatic rocks in the area near LNGS, is responsible for this difference.Comment: 45 pages, 5 figures, 12 tables; accepted for publication in GC

Population Genomics of the Blue Shark, Prionace glauca, Reveals Different Populations in the Mediterranean Sea and the Northeast Atlantic

Populations of marine top predators have been sharply declining during the past decades, and one-third of chondrichthyans are currently threatened with extinction. Sustainable management measures and conservation plans of large pelagic sharks require knowledge on population genetic differentiation and demographic connectivity. Here, we present the case of the Mediterranean blue shark (Prionace glauca, L. 1758), commonly found as bycatch in longline fisheries and classified by the IUCN as critically endangered. The management of this species suffers from a scarcity of data about population structure and connectivity within the Mediterranean Sea and between this basin and the adjacent Northeast Atlantic. Here, we assessed the genetic diversity and spatial structure of blue shark from different areas of the Mediterranean Sea and the Northeast Atlantic through genome scan analyses. Pairwise genetic differentiation estimates (FST) on 203 specimens genotyped at 14,713 ddRAD-derived SNPs revealed subtle, yet significant, genetic differences within the Mediterranean sampling locations, and between the Mediterranean Sea and the Northeast Atlantic Ocean. Genetic differentiation suggests some degree of demographic independence between the Western and Eastern Mediterranean blue shark populations. Furthermore, results show limited genetic connectivity between the Mediterranean and the Atlantic basins, supporting the hypothesis of two distinct populations of blue shark separated by the Strait of Gibraltar. Although reproductive interactions may be limited, the faint genetic signal of differentiation suggests a recent common history between these units. Therefore, Mediterranean blue sharks may function akin to a metapopulation relying upon local demographic processes and connectivity dynamics, whereby the limited contemporary gene flow replenishment from the Atlantic may interplay with currently poorly regulated commercial catches and large-scale ecosystem changes. Altogether, these results emphasise the need for revising management delineations applied to these critically endangered sharks

Nubia-Eurasia kinematics: an alternative interpretation from Mediterranean and North Atlantic evidence

It is argued that the Plio-Quaternary deformation pattern in the Mediterranean region is compatible with a SSWNNE convergence between Africa (Nubia) and Eurasia and that the significant difference between this kinematics and the one provided by global models (SSE-NNW convergence e.g., the NUVEL-1) may be due to the fact that those models interpret North Atlantic data by adopting an oversimplified two-plate configuration, which cannot account for the occurrence of significant seismotectonic activity inside the presumed Nubia and Eurasia blocks. It is shown that the adoption of a new plate configuration involving the Iberia and Morocco microplates, strongly suggested by geological and seismotectonic evidence, makes it possible to identify a kinematic model compatible within errors with the constraints recognized in the Mediterranean region and with the NUVEL-1 North Atlantic data set. Some considerations are made about why the present-day Nubia-Eurasia kinematic models inferred from geodetic observations are significantly different from long-term models, such as model NUVEL- 1 and the one proposed in this work